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<h1>Popitam Help</h1>
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<a name="top"></a>
<table style="width: 100%; text-align: center;" border="1">
  <tbody>
    <tr>
      <td><a href="#formhelp">Form help</a> </td>
      <td><a href="#outputhelp">Output help</a> </td>
    </tr>
  </tbody>
</table>
<h1><a name="formhelp"></a>Form help</h1>
<br>
<ol>
  <li>
    <h2><a name="examples"></a>About the examples</h2>
    <br>
    <ol>
      <li>Example 1 comprises five spectra of peptides with one oxidation on methionine, or with one cystein carbamidomethylation.<br>
        <br>
        <ul>
          <li>LFPLIQAM[ox]HPTLAGK (P1194)<br>
          </li>
          <li>LC[cam]YVALDFEQEMATAASSSSLEK (P63261)<br>
          </li>
          <li>SAEFLLHM[ox]LK (P18621)<br>
          </li>
          <li>DIVNM[ox]LM[ox]HHDR (P11216)<br>
          </li>
          <li>LC[cam]YVALDFEQEMATAASSSSLEK (P63261)<br>
            <br>
          </li>
        </ul>
      </li>
      <li>Example 2 comprises one spectrum of a peptide with two cystein carbamidomethylations.<br>
        <br>
        <ul>
          <li>VFNC[cam]ISYSPLC[cam]K (Q9GZL7)<br>
          </li>
        </ul>
        <br>
      </li></ol></li>
      <a href="#top">Top</a> <li>
        <h2><a name="data"></a>Data file</h2>
Browse your computer's hard disk to find the file containing the 
MS/MS peak list(s) to submit. Take care of selecting the appropriate 
format (mgf, dta) in the format field. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="dataformat"></a>Data file format</h2>
Popitam accepts two formats: mgf (used by Mascot), dta (used by Sequest).<br>
Please note that in mgf, the headers are not read by Popitam.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="database"></a>Database</h2>
Choose one or several databases (use the shift or ctrl keys to make
multiple selections). Please note that Popitam does not use annotations
about post-translational modifications in the database annotations. </li>
      <br>
      <a href="#top">Top</a> <li>
       <h2><a name="aclist"></a>AC list</h2>
Indicate in this box a list of protein accession number (ACs) separated by spaces, to use
as a filter.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="instrument"></a>Instrument</h2>
Specify the type of mass spectrometer that was used to collect the data.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="fragmenterr"></a>Fragment error</h2>
Specify an error tolerance (in Dalton) for MS/MS fragment ion mass values. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="exmodifs"></a>Expected post-translational 
        modifications (fixed, variable)</h2>
These options are not available for the moment. If your data 
contain amino acids with chemical modifications, the latter 
will be treated as unexpected modifications.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="enzyme"></a>Enzyme</h2>
Choose one digestion enzyme in the given list. Available enzymes are: 
Trypsin, LysC, LysN, CNBr, ArgC, AspN, AspN + GluN, AspN + LysC, 
AspN + GluN + LysC, GluC bicarbonate, GluC phosphate, 
Chymotrypsin Low, Chymotrypsin High, Tryp + Chymo, Pepsin pH 1.3, 
Pepsin pH > 2, and Proteinase K.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="missedcleav"></a>Missed-cleavage</h2>
Specify 1 if you want to analyse peptides with 1 missed cleavage or 0 instead. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="scoring"></a>Scoring file (scenario scoring functions)</h2>
Popitam provides the possibility to define an own 
<a href="glossaire.html#functions">scenario scoring function</a>,
as long as it is written in the appropriate format and based on
Popitam's <a href="glossaire.html#functions">subscores</a>. 
Customized scoring functions can then be tested using the web interface.</li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="modGapNb"></a>modGap number</h2>
Popitam builds scenarios with 1 or 2 modGaps and allows to identify 
peptides with one or more modifications. Specify here the wanted number 
(1 or 2) of <a href="glossaire.html#modGaps">modGaps</a> in the scenarios. <br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="parenterr"></a>Precursor mass range</h2>
Allowed deviation (in Dalton) between the precursor mass from the
spectrum and the mass of candidate peptides from the database.
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="gapmass"></a>modGap mass range</h2>
Specify the mass range (in Daltons) of the <a href="glossaire.html#modGaps">modGaps</a>. <br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="toppeptides"></a>Number of displayed peptides</h2>
Choose the number of peptides to display in the results for each spectrum. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="mail"></a>Email address</h2>
Specify your email adress if you wish to receive the results by email. </li>
      <br>
      <a href="#top">Top</a>
    </ol>
    <br>
    <br>
    <h1><a name="outputhelp"></a>Output help</h1>
    <br>
    <ol>
      <li>
        <h2><a name="processed"></a>Total number of protein processed</h2>
Total number of proteins in the chosen database.<br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="pdigestion"></a>Peptides obtained after digestion</h2>
After theoretical digestion of proteins, this line gives the
number of obtained peptides. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="panalyze"></a>Candidate peptides presented for
further analysis</h2>
Number of peptides that passed through the <a
 href="help.html#parenterr">precursor mass filter</a>. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="pscenario"></a>Candidate peptides with one or more
valuable scenarios</h2>
Number of peptides that lead to an identification score. </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="statsize"></a>Sample size for statistics</h2>
Size of the set of peptides used to compute the <a
 href="help.html#pvalue">p-value</a>.<br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="scores"></a>Output scores</h2>
Popitam's output includes three scores: <br>
        <ol>
          <li><span style="font-weight: bold;"> the <a href="help.html#outputscore">scenario score</a></span> which is
computed using one of the three complexe <a href="./glossaire.html#functions">functions</a> learned by <a
 href="glossaire.html#geneticProgramming">Genetic Programming</a> or
the
user specified scoring function </li>
          <li><span style="font-weight: bold;">a <a
 href="help.html#deltascore">delta score</a></span> (comprised between
0
and 1) which is based on the difference between the score and the next
ranked score (similar to Sequest's deltaScore). <br>
          </li>
          <li><span style="font-weight: bold;">a "pseudo" <a
 href="help.html#pvalue">p-value</a></span> (comprised between 0 and
1)
which gives an idea of the deviation between the score of the peptide
and the distribution of scores.<br>
            <br>
          </li>
        </ol>
In Popitam, result validation cannot be based only on the p-value, but
also requires manual interpretation. <br>
        <span style="font-weight: bold;">At the moment, the best way to
distinguish correct matches from random ones is to consider several
parameters, including the distribution of high-ranked peptides, the
proposed scenario and the reported mass shifts associated with modGaps.
        </span><br>
        <br>
      </li>
      <li>
        <h2><a name="outputscore"></a>Scenario score</h2>
The scenario score is computed using one of the complexe <a href="./glossaire.html#functions">functions</a> learned by <a
 href="glossaire.html#geneticProgramming">Genetic Programming</a> or
the
user's specified scoring function. <br>
It measures how the <a href="./glossaire.html#runjumppath">run-and-jump</a>
path found by Popitam can fit the candidate peptide sequence. <br>
        <br>
      </li>
      <a href="#top">Top</a> <li>
        <h2><a name="deltascore"></a>Delta score</h2>
The deltaScore for a given peptide is obtained by dividing the score of
the next ranked peptide by the score of the peptide. For the last
peptide, the deltaScore cannot be computed and is replaced by '-'.<br>
        <br>
        <a href="#top">Top</a> </li>
      <li>
        <h2><a name="pvalue"></a>p-value</h2>
The p-values mirrors the probability of obtaining a score
greater or equal to an observed score in a given distribution by chance.<br>
In Popitam, it is computed on-the-fly from the mean and variance of the
score distribution (the distribution is assumed to be gaussian). As we
are not guaranteed that the negative distribution is actually gaussian,
the value reported by Popitam is not a 'true' probability, but a
measure that gives an idea of the deviation between the score of the first
ranked peptide and the score distribution. In addition, when the AC
filter is used, the statistics are often not sufficient to compute
meaningfull p-values. <span style="font-weight: bold;"><br>
Therefore, Popitam's p-value has to be considered with precaution, and
the decision to accept or reject a match should not be based on the
sole
p-value. </span><br>
When a small number (less than 20) of candidate peptides have been
scored, the p-value is not computed and replaced by '-'. The size of
the score distribution is indicated in the output (<span
 style="font-style: italic;">sample size for statistics</span>). <br>
        <br>
        <a href="#top">Top</a> </li>
      <li>
        <h2><a name="outputmass"></a>Mass</h2>
The reported mass is the monoisotopic mass (Mr) computed for the theoretical peptide.<br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="outputdelta"></a>Delta mass</h2>
Deviation between the observed precursor mass (experimental mass) and
the mass of the theoretical peptide.<br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="result"></a>Spectrum interpretation (Peptide / scenario (shifts))</h2>
The spectrum interpretation column gives the best <a
 href="./glossaire.html#scenario">scenario</a> found by Popitam for the
theoretical peptide. <br>
        <br>
      </li>
      <a href="#top">Top</a> <li>
        <h2><a name="idaclist"></a>Found in ID(AC)</h2>
List of all the proteins in selected database where the peptide has been found.<br>
      </li>
      <br>
      <a href="#top">Top</a> <li>
        <h2><a name="noresult"></a>What if Popitam cannot find any result ?</h2>
The most current explanations are:
        <ul>
          <li>Parameters are too restrictives, try again with broader ranges.</li>
          <li>If you used AC filter, please check that the AC you gave are in the selected database.</li>
        </ul>
      </li>
      <br>
      <a href="#top">Top</a>
    </ol>
  </li>
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